The suit, filed in State Supreme Court on behalf of the teachers’ union and parents with children at Manhattan and Brooklyn schools, argues that the city needed approval from local school boards before it decided to close neighborhood schools and hand their buildings over to charters. Those schools are publicly financed but managed independently, and generally admit students via lottery.

The three schools mentioned in the suit — Public School 194 and Public School 241 in Harlem and Public School 150 in Ocean Hill-Brownsville — were marked for closing late last year because of poor academic performance and lack of popularity with local residents. Education officials offered the families of children attending those schools priority in admission to the charter schools as well as to schools in nearby zones.

The suit said those changes amounted to a redrawing of neighborhood lines and should have been approved by the local board, known as the Community Education Council.

A spokeswoman for the Department of Education declined to comment on the lawsuit or to discuss the broader issue of charters and zoning.

The lawsuit accuses the department of “utilizing its powers over school creation to alter attendance zones unilaterally without the consent or involvement of the people the community school serves,” and adds that it “continues to act by fiat.”

Randi Weingarten, president of the teachers’ union, said in a written statement, “Parents should have a voice when it comes to their children’s education, and by eliminating community schools without public hearings, the D.O.E. is taking away that voice.”

Donna Lieberman, executive director of the New York Civil Liberties Union, said in an interview that the failure to seek approval showed that city officials do “not respect the law and the constraints that have been put on their authority.”

“What has been done here is the elimination of attendance zones basically without any consultation or approval,” she said.

The three schools would be the first in the city to be wholly replaced by charter schools. (Up to now, when new charters are opened in existing school buildings, they have occupied a floor or two alongside their traditional counterparts.)

The transition raises tricky legal questions, since charter schools are generally not permitted to discriminate in admissions, though Chicago and Washington have experimented with favoring neighborhood children in admissions. Already, the Harlem Success Academy, which is scheduled to move into the P.S. 241 building, has revised its charter to give priority to students from failing schools in the area.

The lawsuit comes amid the broader debate over whether the State Legislature should renew the 2002 law giving New York’s mayor control of its schools, which expires in June. Since the mayoral takeover, the local school boards have declined in influence, with zoning among their few remaining powers.

“This is our last shred of authority,” noted Jennifer Freeman, a member of the education council that represents much of Harlem, and a plaintiff in the suit.

Ms. Freeman said she did not oppose charter schools but would have liked to have had a constructive exchange with education officials before a final decision was made.

“I would love to have a public process where the community could understand better what we hope to get from charter schools — why this one was chosen over others,” she said. “I would like to be able to air these issues in the open.”

She also faulted the city for failing to consult local school boards before deciding to close schools, and she said the city did not give the community notice about a public hearing on the charter school plan.

Betsy Gotbaum, the city’s public advocate, is also a plaintiff in the suit.

The lawsuit could throw a wrench into what seemed to be an attractive strategy to encourage the growth of charter schools, an educational model that has earned steady praise from Mayor Michael R. Bloomberg and his schools chancellor, Joel I. Klein.

An important obstacle to fledgling charter programs is acquiring space. Traditional public schools generally do not have to worry about money for facilities, which comes from the district, but charter schools only get money for operations. That means charter operators often struggle to find buildings they can afford, especially in pricey urban markets like New York City, and have to raise funds aggressively to pay for space.

“Finding suitable space for an expanding charter school is one of the greatest challenges we’ve got,” said Nelson Smith, president and chief executive of the National Alliance for Public Charter Schools. “It’s a major constraint on our growth.”

Mr. Smith said that 15 states allow charter schools to receive public funds for facilities. Many charter schools across the country face resistance from public school districts that have watched the rise of charter schools with caution, worried that they might draw away dollars and talented students from other local schools.

A version of this article appears in print on , on page A26 of the New York edition with the headline: Suit Challenges City Plan To Replace Three Schools. Order Reprints|Today's Paper|Subscribe